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The goal of our research is to develop environmentally sound disease management strategies that are economically feasible for Indiana growers producing apples. Our research effort is directly tied to our extension work, and focuses on the identification and management of fungicide resistance in Venturia inaequalis, the fungus that causes apple scab. Apple scab is one of the most serious diseases of apple and ornamental flowering crabapple, and affects both leaves and fruit; losses of up to 100% have been known to occur when apple scab is unmanaged. In commercial apple production, foliar infection by the apple scab pathogen results in defoliation that leads to a loss of apple quality, and impacts winter-hardiness. Fruit infections result in blemished and deformed fruit that cannot be sold. In commercial apple production, this disease is primarily managed through the use of fungicides. However, fungicide resistance is an emerging problem. We are currently surveying the V. inaequalis population for the presence of fungicide resistance. Use of these fungicides continues despite decreasing efficacy, and we have identified increasing shifts in resistance in the scab populations in Indiana and Michigan over the past three seasons, culminating in the development of field resistance and fungicide failures in orchards in both states. Combining field and laboratory assessments has allowed us to develop methods to quickly assess fungicide resistance, and anticipate which orchards are at risk of fungicide failure, thereby helping growers adjust their management programs appropriately. Although fungicide use is the primary means of disease management in commercial apple production, both sustainable apple production and landscape crabapple management relies upon plant disease resistance. However, resistance genes, like some fungicides, have a history of losing their effectiveness over time (“resistance breakdown”). We evaluated 33 years of data on 287 crabapples for long-term scab resistance. Of 287, only 31 had no symptoms of scab for longer than a 10-year period and were identified as resistant to the disease. Of these 31 resistant accessions, 14 eventually displayed symptoms, presumably as a result of infection by one or more newly present races of the pathogen in the trial plot. Notable resistance breakdowns in accessions previously classified as resistant include the development of scab on M. x ‘Prairifire’, M. x ‘Bob White’, M. x ‘Red Jewel’, and M. floribunda. Corresponding to these changes in resistance is the putative development of new V. inaequalis races in North America: Race 5, possessing virulence to the Vm gene in ‘Prairifire’ and the first identification and report of scab on a M. floribunda population that was previously characterized as durably resistant. The detection of scab on this species suggested the presence of Race 7 in North America for the first time, and led to the identification of scab on Malus floribunda 821, the most important source of monogenic scab resistance (Vf) that has been bred into 90 of 110 scab-resistant cultivars and used for transgenic resistance in popular commercial apple cultivars. Our research focuses on evaluating Vf-resistant cultivars to identify which are most susceptible to infection by the new race of scab, and to help growers properly manage these cultivars to minimize the risk of further resistance breakdown. (Hort Science 44:599-608)

Dr. Jody Banks studies the unique biology of lower vascular plants. Her research focuses on three areas that provide important insights into the evolution of developmental and adaptive traits in plant, especially those that cannot be understood by studying angiosperm model systems. The first research area is sex determination in gametophytes of the fern Ceratopteris richardii. Dr. Banks’ group has identified more than 100 mutants of Ceratopteris that affect the sex of the gametophyte. By comparing the phenotypes of single and different combinations of double or triple mutants, they have ordered these genes into a sex-determining pathway. They are now attempting to clone these genes to understand this pathway at the molecular level. The second research area is on arsenic hyperaccumulation in the fern Pteris vittata. In collaboration with Dr. David Salt’s group at Purdue University, they have characterized two genes likely to be involved in arsenic metabolism in this plant. The third research area deals with the genome sequence of the lycophyte Selaginella moellendorffii and its comparison to other plant genomes. Dr. Banks discovered that this plant has the smallest known plant genome (110Mbp). Because of its phylogenetic position (between bryophyes and ferns) and small genome size, the Joint Genome Institute agreed to shotgun sequence this genome. The whole genome sequence was released by the Joint Genome Institute in December 2007.

Dr. Zhixiang Chen’s research interests are in two related areas of plant defense responses. The first area concerns transcriptional and post-transcriptional regulation of plant-pathogen interactions. A major focus in this area is on a family of plant transcription factors containing the novel WRKY zinc-finger DNA-binding motifs. Genetic and molecular approaches are being utilized to understand the roles, regulation, and action mechanisms of plant WRKY transcription factors in plant disease resistance. Other research in the area is aimed at understanding transcriptional and post-transcriptional regulation of plant-virus interactions. Specific projects include analysis of host transcription factors recruited by plant pararetroviruses for activation of viral transcription and plant RNA-dependent RNA polymerases in plant antiviral defense. The second research area deals with salicylic acid (SA)-mediated plant defense responses. Although the role of SA in plant defense has been extensively studied, SA synthesis and perception by plant cells have not been fully elucidated. In addition, plants differ greatly in both basal SA levels and SA responsiveness, and the underlying molecular basis for the great variation among plant species is unclear. Dr. Chen’s group is investigating several Arabidopsis mutants deficient in pathogen-induced SA accumulation. Some of the mutants may result from mutations of genes encoding enzymes required for SA biosynthesis and are useful to elucidate the SA biosynthetic pathways in plants. They are also studying a SA-binding protein that may play a role in SA signal perception and contribute to the variation of SA responsiveness among plant species. These studies will help understand the fundamental mechanisms of plant disease resistance and provide potential targets for disease control in crop plants.

Dr. Kevin Gibson’s research has focused on the development of weed management systems that increase the competitive ability of crops, reduce the need for herbicide inputs, and provide sustainable weed control in agronomic and vegetable crops. He is currently assessing alternative control strategies such as cover crops and intercropping to limit seed rain and reduce the need for herbicide use in vegetable crops. Dr. Gibson is also interested in the distribution, abundance, and management of invasive plants. He has conducted research on the population dynamics and management of garlic mustard, an exotic invader of forests, that suggests that garlic mustard establishment is highly dependent on early season emergence.

Dr. Peter Goldsbrough’s research program is focused on two multigene families in Arabidopsis - metallothioneins (MTs) and glutathione S-transferases (GSTs). Metallothioneins are small metal binding proteins encoded by a small gene family. Recent studies with MT-deficient mutants indicates that MTs are involved in the accumulation of copper and zinc in various tissues including roots and shoots, and the redistribution of these metals during senescence and seed development. The primary reaction catalyzed by GSTs is conjugation of glutzthione to a toxic substrate. We have been studying how herbicide safeners induce the expression of GSTs and other components of the xenobiotic detoxification system, and how GSTs can be used to enhance herbicide tolerance in transgenic plants.

Dr. Steve Goodwin’s research is to understand the genetic bases of plant host-pathogen interactions, at both the molecular and population levels. This information will be used to increase the level of resistance in cereal crops to foliar diseases caused by fungi. Septoria tritici blotch of wheat, caused by Mycosphaerella graminicola (anamorph: Septoria tritici), is an economically important disease that occurs throughout the world. Goodwin has developed microsatellite markers for this fungus that can be used to analyze its population and evolutionary genetics in Indiana and surrounding states to reveal the primary sources of inoculum, the extent of gene flow among populations, and the modes of reproduction during epidemics. Recently, Goodwin worked with collaborators to obtain the complete genomic sequence of this fungus and that of its relative, the black Sigatoka pathogen, M. fijiensis, plus 40,000 EST sequences from M. fijiensis and the related maize pathogen Cercospora zeae-maydis. Work is now proceeding to annotate the nuclear and mitochondrial genome sequences of these pathogens. Comparative genomics analyses identified differences in the gene contents of organisms adapted to wheat versus non-wheat hosts and identified numerous targets for future research. Microarrays developed from the genomic sequences will be used to analyze gene expression under a variety of conditions. On the host side, five genes for resistance to Septoria tritici blotch were mapped in wheat and markers were identified that can be used for marker-assisted selection. Analysis of gene expression revealed that resistant wheat lines have early and late peaks of gene induction; the late peaks begin 14-16 days after inoculation and have not been reported in other hosts. Work is under way to understand the mechanisms of resistance and particularly of the late response. Populations are being developed to facilitate the eventual cloning and molecular characterization of wheat genes for resistance to this pathogen.

Dr. Nick Carpita’s research objectives are to characterize the structural and functional architecture of the plant cell wall, to understand the biochemical mechanisms of biosynthesis of its polysaccharides, and to identify the genes that encode the molecular machinery that synthesizes these components. Specific projects include identifying and characterizing cell wall mutants in Arabidopsis and maize by Fourier transform infrared spectra. Potential mutants identified by this novel spectroscopic method are characterized genetically to determine heritability. A systematic protocol was devised to use biochemical, cytological, and spectroscopic methods to characterize the function of cell-wall biogenesis-related genes in Arabidopsis and maize identified through the mutant screen. Dr. Carpita’s group is classifying mutants by artificial neural networks as a database to classify genes of unknown function. They also develop methods to investigate the biosynthesis and topology of cellulose and the mixed-linkage (1→3),(1→4)-β-D-glucan in maize. They use proteomic and immunological approaches to identify the catalytic machinery and its associated polypeptides. We have also begun a program to characterize the regulation by microRNAs and naturally occurring small interfering RNAs of cellulose synthases and suites of similarly regulated genes in networks that form primary and secondary walls. Finally, we desire to apply our knowledge of cell wall biology to solve practical problems in agriculture. Understanding wall composition and architecture and the regulation of the synthesis of its components is an essential tool in enhancing biomass quality and quantity for biofuel production.

Dr. Charles Woloshuk’s research is focused on problems related to mycotoxins produced by phytopathogenic fungi of maize. Research on Fusarium verticillioides has led to the discovery of several genes that are important for fumonisin production during the colonization of maize kernels. One of these genes (FST1) impacts fumonisin production, fungal development, and pathogenicity. The hypothesis is that FST1 functions as an environmental sensor. The current focus of the research is to examine protein structure and function, and to discover other genes linked with FST1 expression. Woloshuk’s lab has investigated genes that are involved in aflatoxin production by Aspergillus flavus, also a pathogen of maize. Current research has focused on the molecular response of maize plants to heat and draught stresses prior to silking. The hypothesis is that there is a molecular signature in the maize leaves that correlates to kernel susceptibility and high aflatoxin contamination. Proving that this signature exists could lead to new management tools. Woloshuk’s lab also has sequenced and assembled a whole genomic database for Stenocarpella maydis. This resource is being used to study several mutant strains that were obtained by Agrobacterium tumefaciens-mediated transformation (ATMT). The current focus of the research is on a gene that has sequence similarity to known histidine kinases. Woloshuk is also part of a collaborative research project on the Purdue Improved Crop Storage (PICS) system. PICS consists of a low-cost bag system that creates a sealed barrier for store grain and results in a low-oxygen environment inside. Farmers in West and Central Africa are using PICS bags to control insect pests. Woloshuk’s research is to determine if the PICS system can prevent Aspergillus flavus growth and aflatoxin production during storage.

Dr. Rick Latin conducts research on the epidemiology and management of turfgrass diseases. His primary focus is on factors that influence fungicide performance. He recently completed a series of research projects that addressed the effects of plant growth regulators and application volume on the efficacy of fungicides for dollar spot control on creeping bentgrass. He also published his work on synergism among fungicides and the residual efficacy of fungicides on creeping bentgrass turf. He and his students are interested in disease appraisal and recently introduced a new assessment scale and standard area diagrams for assessing dollar spot severity. The current direction of his research has turned towards describing interactions between fungicides and biopesticides and a project to evaluate fungicide resistance among populations of the dollar spot pathogen (Sclerotinia homoeocarpa) throughout Indiana.

Dr. Guri Johal’s interests and expertise are in maize pathology and genetics, and he is involved in three areas of research. The first concerns maize’s interaction with Cochliobolus carbonum, which causes a lethal leaf blight and ear mold disease. A key factor in this pathosystem is HC-toxin, a cyclic tetrapeptide, which is absolutely needed by the pathogen to colonize maize tissues. Exactly how HC-toxin evades maize defenses remains elusive, and unlocking this mystery using a combination of genetic, genomic and molecular approaches constitutes a major thrust of the Johal lab. Efforts include an investigation into the evolutionary origin of the Hm1 disease resistance gene. This gene evolved naturally in maize and it confers complete resistance to C. carbonum by inactivating HC-toxin. An allele of Hm1 confers adult plant resistance, as does the functional allele at the hm2 locus. Why and how these genes behave this way is also pursued. Dr. Johal’s second project concerns a class of mutations that are collectively known as disease lesion mimics (DLMs). These mutants are recognized by their ability to produce symptoms that mimic those that are normally produced during maize’s encounter with various pathogens. The Johal lab has contributed substantially in revealing the biological underpinnings some of these DLMs and is continuing to do so for more and more of these mutants. In addition, DLMs are being used as reporters to uncover natural variation capable of suppressing or enhancing their severity. The cloning and characterization of such natural variants are expected to provide valuable tools and targets for coping with a variety of stresses, both biotic and abiotic. The third project area concerns genes and mechanisms that impact the height and quality of the maize stalk. Again, the approach is to generate and/or identify natural mutants that compromise these stalk traits. The genes underlying these variants are then cloned either by transposon tagging or by map-based cloning approaches. Two recent accomplishments in this area include the cloning of the brittle stalk -2 (bk2) and brachytic-2 (br2) genes. While bk2 encodes a COBRA-like protein required to assemble secondary cell walls, br2 encodes a multidrug resistance protein involved in the polar movement of auxins from the top of the plant to the bottom. An ortholog of the br2 gene was shown to be defective in the sorghum dw3 mutant, which despite its instability has been used extensively in sorghum breeding programs. The molecular mechanism underlying dw3 instability and ways to correct it were also revealed.

Dr. Sue Loesch-Fries’ research is to determine the roles of virus genes in virus replication and in disease development, with the expectation that the results will lead to novel approaches for virus control. Loesch-Fries’ group works with alfalfa mosaic virus (AMV), an important pathogen of legumes, with focus on host and virus proteins involved in the formation of replicase complexes, which are factories where AMV RNAs are synthesized. The yeast two-hybrid system was used to identify proteins in susceptible Arabidopsis plants that are potential interaction partners of the virus proteins. These proteins and the virus proteins have been tagged with fluorescent markers such as the green fluorescent protein to determine protein-protein interactions and localization of host and virus proteins in infected cells by confocal microscopy.

Dr. Jin-Rong Xu works with the rice blast fungus Magnaporthe grisea and the wheat scab fungus Fusarium graminearum. Rice blast is one of the most severe diseases on rice and has become a model to study fungal-plant interactions. Current efforts are focused on the signal transduction pathways regulating infection-related morphogenesis and infectious growth. The main project includes characterization of the PMK1 (Pathogenicity MAP Kinase 1) MAP kinase pathway that controls appressorium formation and plant infection. Several key components of the PMK1 pathway, including an adaptor protein, a MAP kinase kinase, a MAP kinase kinase kinase, a Ras homolog, a transcription factor, and a G-beta subunit of trimeric G-proteins, have been characterized. He also is a member of the International Rice Blast Genome Initiative and actively participates in functional genomics studies of rice-Magnaporthe interactions. The wheat scab fungus is a less studied but important pathogen that has caused devastating epidemics recently in the U.S. Besides reducing yield, F. graminearum produces a variety of mycotoxins, including vomitoxin. Xu and his collaborators have sequenced the F. graminearum genome and developed a whole-genome microarray. These genomic resources have been used to study the interaction of F. graminearum with wheat and barley. He is particularly interested in characterizing genetic mechanisms that regulate plant infection and toxin production in F. graminearum.

The overall goal of Dr. Kiersten Wise’s research program is to develop economical and sustainable disease management practices for agronomic field crops. This is achieved by studying the effects of management techniques on the biology of plant diseases. Through this research we can select management practices that will improve crop production efficiency and simultaneously increase our awareness of how diseases interact with their hosts.

Dr. Mary Alice Webb’s research interests center around accumulation of crystalline calcium oxalate by plants. Her research has focused on understanding how plants synthesize raphides, crystals with a needle-like morphology that deters herbivory. Previous research examined the structure and development of the raphides and the specialized cells that produce them. Dr. Webb developed a method to isolate raphides along with their associated intravacuolar organic matrix from grape leaves, enabling characterization of matrix structure and biochemistry. The goal of these studies has been to identify and define the role of specific matrix components in crystal initiation and growth within plant cells. Recent research has employed proteomics methodology in a broad approach to identify raphide-associated proteins, and key proteins identified via this method have been selected for further study. For example, Dr. Webb’s laboratory has identified and cloned a cDNA for a putative oxalate transporter from grape with substantial homology to the human oxalate transporter Slc26a6. Future studies include examining its localization in relation to raphide development and assaying its ability to transport oxalate. In another project Dr. Webb’s lab has examined calcium oxalate formation in kidney-like organs, Malpighian tubules, in larvae of silkworm (Bombyx mori). Unlike calcium oxalate stones in human kidneys, calcium oxalate crystals in Malpighian tubules of silkworm accumulate throughout the larval stage of the life cycle with no apparent harm to the organism. However, structural and biochemical studies of the tubules and their content have revealed that they share common features with human kidneys, indicating that silkworm larvae could provide a simple model system for examining aspects of kidney stone formation.

Dr. William Johnson’s research program has focused on development weed management systems that integrate cultural practices with judicious herbicide use, improve efficiency of production, and minimize selection pressure for herbicide-resistant weeds. Current research areas include the early detection of herbicide resistant biotypes, particularly those with glyphosate-resistance, biology and management of resistant populations, and the effect of no-till systems on weed communities and on other pests, such as nematodes.

Dr. Zhixiang Chen’s research interests are in two related areas of plant defense responses. The first area concerns transcriptional and post-transcriptional regulation of plant-pathogen interactions. A major focus in this area is on a family of plant transcription factors containing the novel WRKY zinc-finger DNA-binding motifs. Genetic and molecular approaches are being utilized to understand the roles, regulation, and action mechanisms of plant WRKY transcription factors in plant disease resistance. Other research in the area is aimed at understanding transcriptional and post-transcriptional regulation of plant-virus interactions. Specific projects include analysis of host transcription factors recruited by plant pararetroviruses for activation of viral transcription and plant RNA-dependent RNA polymerases in plant antiviral defense. The second research area deals with salicylic acid (SA)-mediated plant defense responses. Although the role of SA in plant defense has been extensively studied, SA synthesis and perception by plant cells have not been fully elucidated. In addition, plants differ greatly in both basal SA levels and SA responsiveness, and the underlying molecular basis for the great variation among plant species is unclear. Dr. Chen’s group is investigating several Arabidopsis mutants deficient in pathogen-induced SA accumulation. Some of the mutants may result from mutations of genes encoding enzymes required for SA biosynthesis and are useful to elucidate the SA biosynthetic pathways in plants. They are also studying a SA-binding protein that may play a role in SA signal perception and contribute to the variation of SA responsiveness among plant species. These studies will help understand the fundamental mechanisms of plant disease resistance and provide potential targets for disease control in crop plants.

Dr. Guri Johal’s interests and expertise are in maize pathology and genetics, and he is involved in three areas of research. The first concerns maize’s interaction with Cochliobolus carbonum, which causes a lethal leaf blight and ear mold disease. A key factor in this pathosystem is HC-toxin, a cyclic tetrapeptide, which is absolutely needed by the pathogen to colonize maize tissues. Exactly how HC-toxin evades maize defenses remains elusive, and unlocking this mystery using a combination of genetic, genomic and molecular approaches constitutes a major thrust of the Johal lab. Efforts include an investigation into the evolutionary origin of the Hm1 disease resistance gene. This gene evolved naturally in maize and it confers complete resistance to C. carbonum by inactivating HC-toxin. An allele of Hm1 confers adult plant resistance, as does the functional allele at the hm2 locus. Why and how these genes behave this way is also pursued. Dr. Johal’s second project concerns a class of mutations that are collectively known as disease lesion mimics (DLMs). These mutants are recognized by their ability to produce symptoms that mimic those that are normally produced during maize’s encounter with various pathogens. The Johal lab has contributed substantially in revealing the biological underpinnings some of these DLMs and is continuing to do so for more and more of these mutants. In addition, DLMs are being used as reporters to uncover natural variation capable of suppressing or enhancing their severity. The cloning and characterization of such natural variants are expected to provide valuable tools and targets for coping with a variety of stresses, both biotic and abiotic. The third project area concerns genes and mechanisms that impact the height and quality of the maize stalk. Again, the approach is to generate and/or identify natural mutants that compromise these stalk traits. The genes underlying these variants are then cloned either by transposon tagging or by map-based cloning approaches. Two recent accomplishments in this area include the cloning of the brittle stalk -2 (bk2) and brachytic-2 (br2) genes. While bk2 encodes a COBRA-like protein required to assemble secondary cell walls, br2 encodes a multidrug resistance protein involved in the polar movement of auxins from the top of the plant to the bottom. An ortholog of the br2 gene was shown to be defective in the sorghum dw3 mutant, which despite its instability has been used extensively in sorghum breeding programs. The molecular mechanism underlying dw3 instability and ways to correct it were also revealed.

Dr. Tesfaye Mengiste’s research focuses on mechanisms of plant resistance to necrotrophic pathogens. The goal of his research is to understand the genetic and the molecular bases of host resistance to necrotrophic pathogens to expedite the breeding of disease resistant cultivars. Using host responses to Botrytis cinerea as a model, genetic components of plant resistance to necrotrophs were identified. B. cinerea is a typical necrotrophic pathogen that causes the gray mold disease in diverse crops. Dr. Mengiste’s research has revealed that plant responses to B. cinerea and other necrotrophic pathogens are regulated by a complex network of interacting genetic, molecular and hormonal factors in the plant. Comparisons of basal resistance to B. cinerea in Arabidopsis and tomato reveal similar resistance in the two plant systems but also differences in disease development. Further, host responses to broad-host necrotrophic fungi reveal a significant cross-talk with plant responses to insect pests and abiotic stress factors. They will continue to use the Arabidopsis and tomato plant systems to further dissect the molecular mechanisms of resistance to Botrytis and investigate how they relate to plant responses to biotrophic pathogens. The molecular and biochemical functions of key genetic components of the plant resistance machinery will be determined. The role of key regulatory proteins in plant disease resistance will be tested using tomato transgenic lines.

Dr. Tesfaye Mengiste’s research focuses on mechanisms of plant resistance to necrotrophic pathogens. The goal of his research is to understand the genetic and the molecular bases of host resistance to necrotrophic pathogens to expedite the breeding of disease resistant cultivars. Using host responses to Botrytis cinerea as a model, genetic components of plant resistance to necrotrophs were identified. B. cinerea is a typical necrotrophic pathogen that causes the gray mold disease in diverse crops. Dr. Mengiste’s research has revealed that plant responses to B. cinerea and other necrotrophic pathogens are regulated by a complex network of interacting genetic, molecular and hormonal factors in the plant. Comparisons of basal resistance to B. cinerea in Arabidopsis and tomato reveal similar resistance in the two plant systems but also differences in disease development. Further, host responses to broad-host necrotrophic fungi reveal a significant cross-talk with plant responses to insect pests and abiotic stress factors. They will continue to use the Arabidopsis and tomato plant systems to further dissect the molecular mechanisms of resistance to Botrytis and investigate how they relate to plant responses to biotrophic pathogens. The molecular and biochemical functions of key genetic components of the plant resistance machinery will be determined. The role of key regulatory proteins in plant disease resistance will be tested using tomato transgenic lines.

Dr. Bob Pruitt’s research is presently focused on two areas that use basic science techniques to address applied problems. The first involves studying the nature of bacterial interactions with plants, with a particular focus on human pathogens that contaminate fresh produce. The goals of this research are to understand how pathogenic bacteria are introduced into the plant system and what bacterial, plant and environmental factors allow them to survive and proliferate. Experiments utilize techniques ranging from traditional microbiology and genetics to modern sequencing methods to examine the microbial communities associated with commercial produce. The second area is to try and develop a modern plant molecular genetic/genomic system to apply to the study of weed science. Availability of a genome sequence together with a comprehensive set of molecular markers would greatly simplify the study of the natural and selected variation in weed traits that affect weed life history as well as those that impact agriculture.

Dr. Emery is interested in the evolution of the ecological niche, and how ecological processes shape the evolutionary trajectories of populations and species. The distribution of a species is largely a reflection of its ecological niche, and a major part of her research aims to understand the ecological and evolutionary processes that shape the distribution patterns that we observe in natural populations. Her research integrates community ecology, population biology, and phylogenetics; Dr. Emery uses field experiments, molecular methods, anatomical techniques, and comparative methods to address a variety of questions about the evolution of the ecological niche in plant populations and species.

Researchers in the Aime lab study all aspects of mycology, from genomics to pathology, although at its core the lab focuses on the earliest diverging lineages of Basidiomycota (Pucciniomycotina, Ustillaginomycotina, and Wallemiomycetes) and on basidiomycetes in tropical ecosystems. Our primary focus is on: (1) Systematics, biology, and evolution of rust fungi: the rust fungi represent the single largest group of plant pathogens with incredibly complex life cycles. Our work in this area uses phylogenetics and genomics to try and understand how these fungi became so successful and to provide tools for their identification. (2) Biodiversity of tropical fungi; it is conservatively estimated that more than 1 million fungal species have yet to be discovered and described by science and that many of these may reside in tropical world regions that have not yet been explored for fungi. Dr. Aime has spent 15 years documenting and describing new species and genera from a very remote region in Guyana and other tropical forests worldwide. (3) Systematics and biology of earliest diverging Basidiomycota, which includes the rust and smut fungal lineages and their non-pathogenic yeast and yeast-like relatives.

Dr. Iyer-Pascuzzi’s research investigates the mechanisms that plant roots use to perceive and respond to the environment. There are two primary areas of research in the lab. The first is focused on understanding the molecular basis of plant resistance to bacterial wilt, caused by Ralstonia solanacearum. Ralstonia is a devastating soil-borne pathogen that first infects root systems. Despite the devastation it causes, little is known regarding the networks that underlie resistance or susceptibility, and root responses to R. solanacearum are unclear. Using both tomato and Arabidopsis, we focus on understanding resistance responses at three levels of root development: root cell types, root developmental stages, and root architecture. Current questions include, what are the spatio-temporal dynamics of pathogen invasion in resistant and susceptible genotypes? How are different root cell types and developmental stages affected by bacterial wilt? What are the gene regulatory networks involved in the response to bacterial wilt within each cell type? We use a combination of cell biology, genetics, and genomics approaches to address these questions. The major goal of this research is to identify novel forms of resistance to bacterial wilt. Our second area of research is centered around the role of Nodule Inception-Like Proteins (NLPs) in root development. NLP proteins are a unique family of transcription factors found in a wide diversity of plant species. We are studying the molecular mechanisms through which these proteins mediate root development and stress responses in Arabidopsis.

Dr. Iyer-Pascuzzi’s research investigates the mechanisms that plant roots use to perceive and respond to the environment. There are two primary areas of research in the lab. The first is focused on understanding the molecular basis of plant resistance to bacterial wilt, caused by Ralstonia solanacearum. Ralstonia is a devastating soil-borne pathogen that first infects root systems. Despite the devastation it causes, little is known regarding the networks that underlie resistance or susceptibility, and root responses to R. solanacearum are unclear. Using both tomato and Arabidopsis, we focus on understanding resistance responses at three levels of root development: root cell types, root developmental stages, and root architecture. Current questions include, what are the spatio-temporal dynamics of pathogen invasion in resistant and susceptible genotypes? How are different root cell types and developmental stages affected by bacterial wilt? What are the gene regulatory networks involved in the response to bacterial wilt within each cell type? We use a combination of cell biology, genetics, and genomics approaches to address these questions. The major goal of this research is to identify novel forms of resistance to bacterial wilt. Our second area of research is centered around the role of Nodule Inception-Like Proteins (NLPs) in root development. NLP proteins are a unique family of transcription factors found in a wide diversity of plant species. We are studying the molecular mechanisms through which these proteins mediate root development and stress responses in Arabidopsis.

Dr. Bryan Young's research focuses on weed biology and ecology relative to developing effective management strategies in agronomic crops, herbicide application technologies for optimization and stewardship of herbicide use, and the physiological characterization of herbicide-resistant weed biotypes. His goal is to bridge the basic and applied aspects of weed management research to assist in delivering more effective weed management recommendations to crop producers and land managers.

Dr. Yoon’s research interest lies in understanding of the molecular mechanisms of the key steps in the phytohormone ethylene biosynthesis and its signaling pathway using the model plant Arabidopsis thaliana. The gaseous hormone ethylene regulates many important plant growth and developmental processes, including seed germination, root hair formation, nodulation, senescence and response to a variety of developmental and environmental stresses. Two main research projects are currently under way in the lab. First is to investigate the molecular mechanism regulating protein turnover in ethylene biosynthesis. Specifically, we are aiming to understand the roles of phosphorylation in protein turnover of the 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS), a key enzyme in the ethylene biosynthesis and the Ethylene Overproducer 1 (ETO1)/ETO1-like (EOL) proteins, ubiquitin ligases that target a subset of ACS for degradation. Besides, we are also interested in identification and characterization of novel proteins regulating ethylene biosynthesis to acquire better insight in the molecular aspects of ethylene biosynthesis regulation. Secondly, we are focusing on elucidation of the roles of Constitutive Triple Response 1 (CTR1), a Raf-like protein kinase that acts as a negative regulator, in the ethylene signaling pathway. Ethylene is perceived by a family of ethylene receptors that are derived from two-component histidine kinase, and the receptors are located at the Endoplasmic Reticulum (ER). Recently, we resolved one of the longstanding questions in the ethylene signaling fields how ethylene signals are transduced from the ER to the nucleus to activate ethylene responsive genes in the nucleus. In the absence of ethylene, CTR1 phosphorylates EIN2, a critical positive regulator in the pathway, which blocks an activating proteolytic cleavage. In response to ethylene, the inactive CTR1 fails to phosphorylate EIN2, which is then cleaved by an unidentified protease, releasing the C-terminal domain that then migrates into the nucleus where it activates the transcription factor EIN3, either directly or indirectly, to regulate ethylene-mediated gene expression. Elucidation of the mechanism for regulating EIN2 in the ethylene signaling pathway bridges the gap between the signaling events from the receptor at the ER to the nucleus. However, this also raises a number of intriguing questions and our lab is particularly interested in understanding: 1) how do the ethylene receptors activate CTR1 in the early step of the ethylene signaling pathway?; 2) how does the ethylene response induced by the activation of EIN2 is turned off in the nucleus?; 3) and what are the roles of CTR1 other than phosphorylating EIN2 at the ER. We use the combination of biochemistry, genetics, cell biology and molecular biology approaches to address these questions.

I am interested in the regulation and evolution of plant transposable elements. Transposable elements, or transposons, are, by far, the most dynamic part of the eukaryotic genome, and the majority, often the vast majority, of plant genomes are composed of these genomic parasites. Although they are an important source of genetic novelty, transposons can also be a significant source of detrimental mutations. Because of this, plants (and indeed all eukaryotes) have evolved a sophisticated “immune system” whose function is to detect and epigenetically silence them. My research centers on determining the means by which transposons are detected and then maintained in a silenced state. To do this, the my lab has focused on MuDR, a transposon in maize that can be reliably and heritably silenced by a naturally occurring derivative of that element. In addition to its role in transposon control, epigenetic silencing is employed by plants and animals for a wide variety of other purposes, and epigenetic silencing pathways in plants are particularly diversified. However, whatever else they do, all of these pathways appear to be involved in transposon silencing as well, making transposons an excellent model for understanding how epigenetic information is encoded and propagated. Finally, transposon mobilization and subsequent silencing can have dramatic effects on the expression of plant genes. Current work in the my lab combines a detailed analysis of MuDR transposon silencing with a global analysis of the effects of transposon silencing on plant gene function and phenotypic variation.